Ditto Caster's comments - once you choose a body style, you'll start adding lenses. After you buy your first couple, it really doesn't make a whole lot of sense to switch brands. They are both extremely good brands so it always comes down to what you choose first. Personal preference is the biggest factor as prices are comparable between the brands.
The only capability difference I've come across yet is that Nikon has an Auto ISO feature that Canon does not. To me, this is a setting that only a few will tinker with and fewer yet would even use on a regular basis. Those who know their camera's capabilities will opt to go with setting ISO and adjusting the other settings. Image sensors are of such excellent quality these days, you can shoot a wide variety of ISO settings and not be able to tell much of a difference under certain lighting conditions so I think Nikon's philosophy was to add a feature because they could. Canon chose not to (that is, unless they've decided to add it). All I know is that in my 1Ds Mark II body, I don't have the Auto ISO setting and even if I did, I'm confident I wouldn't use it because I'm a control freak. I leave very little up to the camera to decide for me.
Good luck with your choice! Check out the online stores: B&H and Adorama... also newegg... They're my top 3 choices for equipment but now and then, I buy stuff from the local pro camera shop to help keep them in biz since I believe there is value in supporting local businesses.